Cloning and sequence analysis of the small subunit ribosomal RNA gene from Nematodirus battus

The small subunit ribosomal RNA gene (SSU rRNA) from the nematode parasite, Nematodirus battus, was cloned from amplified genomic DNA using polymerase chain reaction primers complementary to the 5' and 3' ends of Haemonchus contortus small subunit ribosomal DNA (SSU rDNA). The 1,758 base pair cloned fragment was sequenced in both directions using internally generated primers and aligned with those from the genus Haemonchus. Results indicated a 1.9% sequence difference between the genera with a 14.2% difference between N. battus and Caenorhabditis elegans. Data presented here in conjunction with previously published work comparing rDNA sequences within the genus Haemonchus demonstrate limited divergence in this group of genes between these subfamilies and suggest further that this molecule alone may be inappropriate for assessing phylogenetic relatedness within the superfamily Trichostrongyloidea.